Microsoft Word

• You can specify it when you create a new rmarkdown document.

• You can also specify it later in the YAML header.

---
title: "rmarkdown_pdf_docx"
author: "Sebastien Renaut"
date: '2018-09-06'
output: word_document
---

• Then, it’s just a matter of kniting the document!

• Little documentation, few options & configurations are possible. (This is not the course of events that should be promoted, as it moves away from an open source environment).

Portable Document Format (.pdf)

• You need a extra step to go from LaTeX (.tex) format to a .pdf. This is handled by the pdflatex function in R.

• LaTeX software is a high-quality typesetting system.

• It is the de facto standard for the communication and publication of scientific documents.

• LaTeX is available as free software.

• Latex software is available here.

• If interested, follow this discussion: Why LaTeX is such a bloated system?

• So…TinyTeX is a custom LaTeX distribution based on TeX Live that is small in size (~150MB) but functions well in most cases, especially for R users .

• tinytex R package is a wrapper function that installs TinyTeX.

Exercice 1 (15min.)

• Install the tinytex R package from the console.

install.packages(“tinytex”)
library(tinytex)
It takes a few minutes to download and compile tinytex (~150MB)
install_tinytex()

• Compile your document as .pdf:

-–
title: “rmarkdown_pdf_docx”
author: “Sebastien Renaut”
date: ‘2018-09-06’
output: pdf_document
-–

More complex header

-–
output
pdf_document:
keep_tex: true
fig_caption: true
latex_engine: pdflatex
title: “This is my first Rmarkdown manuscript”
date: February 07, 2019
geometry: margin=1in
fontfamily: mathpazo
fontsize: 11pt
spacing: double
csl: ../reference_material/peerj.csl
bibliography: ../reference_material/reference.bib
-–

• Note the indentation in the .Rmd document.

• Note the bibliography file and csl file for formatting references.

Exercice 2: R packages rticles (10min.)

• This is a nice package to format articles according to the specification of a journal.

• But first, you need to install it in the R console install.packages("rticles").

```{r rticles, include=T}
#install.packages(“rticles”)
library(rticles)
```

• Once installed, try starting a new R markdown document according to your journal of interest.

Template (.tex)

• You can build your own template if you know Latex…

• There are many templates available on the web that you can use.

• Here is one I like for manuscripts (Thanks svmiller!):

• Here is one I like for CVs:

• Simply download it and add it to the YAML header like this: template: ../reference_material/svm-latex-ms.tex

-– output:
pdf_document:
keep_tex: true
fig_caption: true
latex_engine: pdflatex
template: ../reference_material/svm-latex-ms.tex
title: "This is my first Rmarkdown manuscript
-–

Overleaf

• Overleaf is an online LaTeX and Rich Text collaborative writing and publishing tool that makes the whole process of writing, editing and publishing scientific documents much quicker and easier.

• Remember this:
  

• So you can generate your .tex file, upload it to a github repo and Overleaf will connect to it. Others can then collaborate and modify the .tex file.

• Let’s take a quick look at overleaf. Once you have an overleaf account, you can connect it to a github repository. You can then pull/push from overleaf to github, allowing others to modify your .tex file.

• A tutorial on how to interface an R Notebook with Overleaf

• How do I connect an Overleaf project with a repo on GitHub, GitLab or BitBucket?

Presentations

• You can also generate Powerpoint-like presentations.
  

Bookdown

• Bookdown is an open-source R package that facilitates writing books and long-form articles/reports with R Markdown.

Radix

• Radix offers a better look for publishing blog, webpages, adapted to mobile devices.
  

• You will need:
  • [Rstudio v1.2][https://www.rstudio.com/products/rstudio/download/preview/].
    
  • radix

```{r radix, echo = T}
install.packages(“radix”)
```

• Change output in header to:

-–
title: “Rmarkdown: radix”
author: “Sebastien Renaut”
output: radix::radix_article
-–

• Then you can start playing with the radix options, such as in this example below (full width figures):

```{r radix_example, echo = F, layout=‘l-screen-inset’}
library(leaflet)
leaflet() %>%
addTiles() %>%
addMarkers(lng=174.768, lat=-36.852,popup=“The birthplace of R”)
```